Figures par molécule

J’ai trouvé ces figures qui permettraient de présenter plus que juste la médiane par molécule…

#Open the datasets

max <- read.csv("data/max.csv")
min <- read.csv("data/min.csv")
mol.med <- read.csv("data/mol.csv")

min$Year <- factor(min$Year)
max$Year <- factor(max$Year)
max$Route <- factor(max$Route)
mol.med$Year <- factor(mol.med$Year)

#Rename Route
max$Route <- ifelse(max$Route=="IM_L", "IMM-Lactation",
                    ifelse(max$Route=="IM_T", "IMM-Tarissement",
                           ifelse(max$Route=="INJ", "Injectable", 
                                  ifelse(max$Route=="IU", "IU", 
                                         ifelse(max$Route=="ORAL", "PO", "Topique")))))
#Categorie 1
library(plotly)
## Le chargement a nécessité le package : ggplot2
## 
## Attachement du package : 'plotly'
## L'objet suivant est masqué depuis 'package:ggplot2':
## 
##     last_plot
## L'objet suivant est masqué depuis 'package:stats':
## 
##     filter
## L'objet suivant est masqué depuis 'package:graphics':
## 
##     layout
fig <- plot_ly(min,
               x = ~Year,
               y = ~POLYMYXINB_SULF_DCD, 
               type = 'box', 
               name="Polymixine B",
               marker=list(color="white")
               )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~CEFTIOFUR_DCD,
                         type = 'box', 
                         name="Ceftiofur",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~DANOFLOXACIN_DCD,
                         type = 'box', 
                         name="Danofloxacin",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~ENROFLOXACIN_DCD,
                         type = 'box', 
                         name="Enrofloxacin",
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~MARBOFLOXACIN_DCD,
                         type = 'box', 
                         name="Marbofloxacin",
                         marker=list(color="white")
                         )


 fig.cat1.mol <- fig %>%
              layout(boxmode="group",
                     title = 'Utilisation des antibiotiques de catégorie I par molécule', 
                     yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                     hoverformat = '.0f',  
                     range = list(0, 90)) #Adjust the y axis range
         )

fig.cat1.mol
## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'
#Categorie 2
fig <- plot_ly(min,
               x = ~Year,
               y = ~GAMITROMYCIN_DCD, 
               type = 'box', 
               name="Gamitromycine",
               marker=list(color="white")
               )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~TILDIPIROSIN_DCD, 
                         name = 'Tildipirosine',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~TILMICOSIN_DCD, 
                         name = 'Tilmicosine',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~TULATHROMYCIN_DCD, 
                         name = 'Tulathromycine',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~TYLOSIN_DCD, 
                         name = 'Tylosine',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~AMPICILLIN_DCD, 
                         name="Ampicilline",
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~NEOMYCIN_SULF_DCD, 
                         name = 'Neomycine',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~STREPTOMYCIN_SULF_DCD, 
                         name = 'Streptomycine',
                         type = 'box', 
                         marker=list(color="white")
                         )


 fig.cat2b.mol <- fig %>%
              layout(boxmode="group",
                     title = 'Utilisation des antibiotiques de catégorie II par molécule (partie 2/2)', 
                     yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                     hoverformat = '.0f',  
                     range = list(0, 4)) #Adjust the y axis range
         )

fig.cat2b.mol
## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'
#Categorie 2
fig <- plot_ly(min,
               x = ~Year,
               y = ~DIHYDROSTREPTOMYCIN_DCD, 
               name = 'Dihydrostreptomycine',
               type="box",
               marker=list(color="white")
               )

fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~CEFAPIRIN_DCD, 
                         name = 'Céphapirine',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~PIRLIMYCIN_DCD, 
                         name = 'Pirlimycine',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~CLOXACILLIN_DCD, 
                         name = 'Cloxacilline',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~BENZYLPENICILLIN_B_DCD, 
                         name = 'Benzylpenicilline B',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~BENZYLPENICILLIN_P_DCD, 
                         name = 'Benzylpenicilline P',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~TRIM_SULFADOXINE_DCD, 
                         name = 'Trimethoprim-sulfa',
                         type = 'box', 
                         marker=list(color="white")
                         )

fig.cat2a.mol <- fig %>%
              layout(boxmode="group",
                     title = 'Utilisation des antibiotiques de catégorie II par molécule (partie 1/2)', 
                     yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                     hoverformat = '.0f',  
                     range = list(0, 160)) #Adjust the y axis range
         )

fig.cat2a.mol
## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'
#Categorie 3
fig <- plot_ly(min,
               x = ~Year,
               y = ~CHLORTETRACYCLINE_DCD, 
               type = 'box', 
               name="Chlortetracycline",
               marker=list(color="white")
               )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~OXYTETRACYCLINE_DCD, 
                         name = 'Oxytetracycline',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~TETRACYCLINE_DCD, 
                         name = 'Tetracycline',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~SUCCINYLSULFATHIAZOLE_DCD, 
                         name = 'Succinyl Sulfathiazole',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~SULFAGUANIDINE_DCD, 
                         name = 'Sulfaguanidine',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~SULFAMERAZINE_DCD, 
                         name = 'Sulfamerazine',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~SULFAMETHAZINE_DCD, 
                         name = 'Sulfamethazine',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~SULFANILAMIDE_DCD, 
                         name = 'Sulfanilamide',
                         type = 'box', 
                         marker=list(color="white")
                         )
fig <- fig %>% add_trace(min,
                         x = ~Year,
                         y = ~SULFATHIAZOLE_DCD, 
                         name = 'Sulfathiazole',
                         type = 'box', 
                         marker=list(color="white")
                         )



 fig.cat3.mol <- fig %>%
              layout(boxmode="group",
                     title = 'Utilisation des antibiotiques de catégorie III par molécule', 
                     yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
                     hoverformat = '.0f',  
                     range = list(0, 20)) #Adjust the y axis range
         )

fig.cat3.mol
## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'